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Table 4 Highly significant GWAS variants (RMIP ≥ 0.25) and their adjacent candidate genes

From: Limits on the reproducibility of marker associations with southern leaf blight resistance in the maize nested association mapping population

Chromosome Physical position (AGPv2) Allelea Effectb P-value RMIP Genic position Inside QTLc Nearest gene ID Position of nearest gene (AGPv2) Annotation
Start End
1 59772038 T/C 0.09 9.4E-10 0.35 Intergenicd N GRMZM2G134671 59764838 59769739 CCT/B-box zinc finger protein
1 90059294 C/T 0.08 8.5E-14 0.35 Intergenic Y GRMZM5G806839 90108398 90107598 AP2 domain containing protein
2 34246559 A/C 0.11 1.8E-16 0.39 Intergenic N GRMZM5G876621 34361966 34343251 IBR domain-containing protein
2 36938074 G/A 0.10 1.4E-22 0.53 3’UTR Y GRMZM2G022627 36936010 36938218 Transducin/WD40 repeat-like superfamily protein
2 204757213 G/A 0.11 4.5E-09 0.41 Intergenic N GRMZM2G142932 204771189 204767728 Basic helix-loop-helix (bHLH) DNA-binding protein
2 207520001 CNV- 0.11 4.4E-09 0.28 Intergenic Y GRMZM2G062156 207635000 207637178 Transporter family protein
3 16574125 T/C 0.12 1.8E-26 0.43 Non-synonymous_codinge Y GRMZM2G463580 16575869 16572429 Leucine-rich repeat transmembrane protein kinase
3 16575842 C/G 0.15 9.7E-14 0.46 5’UTR Y
3 32885733 C/T 0.19 9.1E-16 0.9 Intergenic Y GRMZM2G132936 32957454 32949608 RNA recognition motif (RRM)-containing protein
3 219885527 T/C -0.11 3.1E-12 0.28 Intronic Y GRMZM2G074572 219900229 219884844 Stomatal cytokinesis defective/SCD1 protein
3 220658469 A/C -0.08 6.0E-12 0.25 Intronic Y GRMZM2G130375 220651805 220659525 Beta galactosidase 1
4 2046350 CGG/--- -0.08 3.8E-09 0.26 Non-synonymous_coding Y GRMZM2G131442 2044016 2047386 MYB domain protein 112
5 164110001 CNV- 0.10 1.5E-11 0.42 Intergenic Y GRMZM2G111872 164120892 164124546 Heavy metal-associated domain containing protein
6 7001531 A/C -0.08 1.1E-15 0.4 Intergenic Y GRMZM2G127342 7036171 7039824 Lysine histidine transporter 1 (LHT1)
7 7958250 +/- -0.08 1.9E-08 0.3 Intergenic Y GRMZM2G021149 7954180 7955128 LSM domain containing protein
7 142997161 G/A 0.09 7.3E-09 0.28 Intergenic Y GRMZM2G091919 143003673 143001781 protein kinase superfamily protein
8 22229116 G/A 0.13 1.3E-08 0.35 Intergenic N GRMZM2G325612 22249167 22245141 Cytokinin oxidase 5
8 62217745 T/A 0.10 6.3E-14 0.34 Intergenic Y GRMZM2G130101 62267220 62273955 Unknown
8 171334544 A/G -0.06 1.2E-09 0.26 Intronic N GRMZM2G476009 171332654 171335508 DNA-directed RNA polymerases subunit RPABC1
9 16263773 A/G 0.17 9.9E-09 0.33 Intergenic Y GRMZM2G301860 16253405 16252231 AP2 domain containing protein
9 16317865 G/A 0.10 1.4E-15 0.59 Down_stream Y GRMZM2G099363 16320573 16318197 Caffeoyl-CoA O-methyltransferase
9 106051436 G/A 0.08 1.7E-05 0.45 Intergenic Y GRMZM2G107886 106201175 106203143 CCT/B-box zinc finger protein
9 139547728 C/G -0.11 3.4E-08 0.32 Intergenic N GRMZM2G402015 139591514 139589475 Plant U-box 13, spotted leaf 11
10 3090835 G/A -0.13 6.2E-10 0.47 Intergenic Y GRMZM2G068465 3066458 3062645 Cytochrome P450
10 64647379 G/A 0.06 5.7E-09 0.53 Intergenic Y NA    
10 134501142 C/T 0.06 4.4E-08 0.77 Intronic Y GRMZM2G063972 134495450 134504022 Heat shock protein DnaJ
  1. aAlleles reported as: “B73 allele/alternate allele”. “CNV-” represents the read depth of a line is significantly lower than B73.
  2. bThe mean effect of each significant SNP across data subsamples.
  3. cSNPs located within model 7 QTL SI are indicated as “Y” and “N” otherwise.
  4. dVariants more than 500 bp away from an annotated gene.
  5. eVariation lies in the coding region and results in an amino acid change.